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Items tagged with "common" (5)

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Workflows (4)

Taverna 1 Original Uploader Paul Fisher	KEGG pathways common to both QTL and microarray based investigations (v3) Created: 24/11/09 @ 17:14:43 \| Last updated: 03/12/09 @ 15:28:49 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype. Example input for this workflow is given below (as newline separated values). qt... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 1 Viewed: 261 times \| Downloaded: 125 times Tags (11): common \| data-driven \| disease \| genotype \| kegg \| microarray \| pathway \| pathway-driven \| pathways \| phenotype \| similarity	View Download (v3)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v1) Created: 15/11/10 @ 12:08:18 \| Last updated: 16/11/10 @ 16:07:49 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 10 times Tags (33): african trypanosomiasis \| binfo \| chromosome \| common \| data-driven \| database \| disease \| ensembl \| entrez \| gene \| gene identifier \| geneid \| genes \| genomic \| genotype \| kegg \| Kegg Pathways \| KeggID \| loci \| locus \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| region \| sleeping sickness \| species \| trait \| trichuris muris \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for RefSeq ids (v1) Created: 15/11/10 @ 12:25:01 \| Last updated: 15/11/10 @ 12:28:12 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to search for pathways in the KEGG pathway database. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 62 times \| Downloaded: 35 times Tags (34): affmetrix \| affymetrix \| bconv \| binfo \| chromosome \| common \| data-driven \| database \| disease \| ensembl \| entrez \| expression \| gene \| gene expression \| gene identifier \| geneid \| genes \| genomic \| kegg \| Kegg Pathways \| KeggID \| microarray \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| species \| swissprot \| trait \| transcribe \| transcription \| trichuris muris \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	KEGG pathways common to both QTL and microarray based investigations (v1) Created: 15/11/10 @ 12:30:21 \| Last updated: 15/11/10 @ 12:30:59 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 20 times \| Downloaded: 14 times Tags (21): affmetrix \| affymetrix \| binfo \| chromosome \| common \| data-driven \| gene expression \| gene identifier \| geneid \| genotype \| kegg \| Kegg Pathways \| KeggID \| microarray \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| trait	View Download (v1)

Packs (1)

Creator:

Paul Fisher

Genotype to Pathway

Created: 11/08/09 @ 14:44:16 | Last updated: 11/08/09 @ 14:52:12

This pack is for investigating links between the genotype of an organisms to possible pathways. This constitutes half of the pathway-driven approach, genotype to pathway, and pathway to phenotype.

18 items in this pack

Comments: 0 | Viewed: 86 times | Downloaded: 7 times

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